Download or read book Computational Biology of Non Coding RNA written by Xin Lai and published by Humana Press. This book was released on 2019-02-04 with total page 390 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume details a collection of state-of-art methods including identification of novel ncRNAs and their targets, functional annotation and disease association in different biological contexts. Chapters guide readers through an overview of disease-specific ncRNAs, computational methods and workflows for ncRNA discovery, annotation based on high-throughput sequencing data, bioinformatics tools and databases for ncRNA analyses, network-based methods, and kinetic modelling of ncRNA-mediated gene regulation. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Biology of Non-Coding RNA: Methods and Protocols aims to provide a state-of-the-art collection of computational methods and approaches that will be of value to researchers interested in ncRNA field.

Download or read book Computational Non coding RNA Biology written by Yun Zheng and published by Academic Press. This book was released on 2018-09-14 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Non-coding RNA Biology is a resource for the computation of non-coding RNAs. The book covers computational methods for the identification and quantification of non-coding RNAs, including miRNAs, tasiRNAs, phasiRNAs, lariat originated circRNAs and back-spliced circRNAs, the identification of miRNA/siRNA targets, and the identification of mutations and editing sites in miRNAs. The book introduces basic ideas of computational methods, along with their detailed computational steps, a critical component in the development of high throughput sequencing technologies for identifying different classes of non-coding RNAs and predicting the possible functions of these molecules. Finding, quantifying, and visualizing non-coding RNAs from high throughput sequencing datasets at high volume is complex. Therefore, it is usually possible for biologists to complete all of the necessary steps for analysis. Presents a comprehensive resource of computational methods for the identification and quantification of non-coding RNAs Introduces 23 practical computational pipelines for various topics of non-coding RNAs Provides a guide to assist biologists and other researchers dealing with complex datasets Introduces basic computational methods and provides guidelines for their replication by researchers Offers a solution to researchers approaching large and complex sequencing datasets

Download or read book Long Non Coding RNA Biology written by M.R.S. Rao and published by Springer. This book was released on 2017-08-16 with total page 323 pages. Available in PDF, EPUB and Kindle. Book excerpt: This contributed volume offers a comprehensive and detailed overview of the various aspects of long non-coding RNAs and discusses their emerging significance. Written by leading experts in the field, it motivates young researchers around the globe, and offers graduate and postgraduate students fascinating insights into genes and their regulation in eukaryotes and higher organisms.

Download or read book Non coding RNAs in Complex Diseases written by Xia Li and published by Springer. This book was released on 2018-09-06 with total page 126 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book offers an in-depth and comprehensive review on current understanding of regulatory ncRNAs in complex diseases from a view of bioinformatics. It conveys state-of-the-art bioinformatics tools and methods for ncRNAs from computational detection, functional prediction, to their roles in diseases. Computational methods used to investigate uncharacterised ncRNAs in diseases are mainly summarized in seven aspects: DNA variation of ncRNAs in diseases, prioritization of disease-related ncRNAs, dysregulation epigenetic factors that regulate ncRNA misexpression (DNA methylation and histone-modification), complex crosstalk across ncRNAs, ncRNAs acted as competing regulators to mediate the expression of protein-coding genes, non-coding RNAs mediated risk pathways,and their contributions to drug target predictions. The generally used data resources of ncRNAs are also listed in the end. This book provides important information on the current progress in the fast-moving fields of bioinformatics for regulatory ncRNAs. It provides a timely and useful reference for computational biologists, specifically with RNA interests, and other related areas. Prof. Xia Li is a Professor and the Dean of College of Bioinformatics Science and Technology, Harbin Medical University, China. Dr. Yun Xiao, Dr. Juan Xu, Dr. Shangwei Ning and Dr. Yunpeng Zhang are from College of Bioinformatics Science and Technology, Harbin Medical University, China.

Download or read book AGO Driven Non Coding RNAs written by Bibekanand Mallick and published by Academic Press. This book was released on 2019-01-20 with total page 387 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ‘RNA world’ hypothesis that proposed RNA molecules as the first form of genetic material was put forwarded in the late 1980s but got impetus only recently when high-throughput sequencing technologies began unearthing new types of non-coding RNA (ncRNA) transcripts in higher eukaryotes. Till then, research on ncRNAs were primarily confined to transfer RNAs and, ribosomal RNAs, which act as the messengers of the protein synthesis and allow translation of genetic information encoded by DNA into proteins. In recent years, the integration of high-throughput genomic technologies with molecular biology and omics sciences have revolutionized the fields of ncRNA research by identifying the hidden treasures of several new types of ncRNAs encoded in the genomes of several organisms and decrypting their versatile roles in gene expression and epigenetics. Among these, two small endogenous ncRNAs, namely microRNAs (miRNAs) and piwi-interacting RNAs (piRNAs) that drive argonaute (AGO) family of proteins namely Ago and Piwi respectively and silence the expression of genes have geared up molecular and disease biology research in recent years. Both miRNAs and piRNAs are expressed in higher eukaryotes, including human and act as cellular rheostats by regulating the expression of significant fraction of genes encoded in the genomes. The aberrant expressions of these small ncRNAs within the cells cause various abnormalities and diseases including cancer. Manipulating their aberrant expression or function can serve as potential novel diagnostic/prognostic biomarkers and bring in new therapeutic strategies for multiple human diseases. This can be further translated from bench-side to clinic for improving human health. This book captures the essence of the pioneering work of some of the world’s leading researchers showcasing the scientific excitements surrounding the evolving regulatory roles of miRNAs and piRNAs highlighting their potential towards the diagnosis and therapeutics of various diseases. The book is geared towards scientists, students, and will particularly appeal to active investigators in RNA biology, molecular biology, cancer research as well as clinicians and will provide them a comprehensive view of recent discoveries and research progresses to utilize miRNAs, piRNAs and their interacting proteins, Ago and Piwi for diagnosis, prognosis and therapeutics of diseases. Provides a unified cutting-edge resource for both miRNAs and piRNAs, two promising AGO-clade small ncRNAs, their functions and potential applications Showcase high-throughput technologies and other approaches for discovery of these small ncRNAs and their targets Unveils the diverse molecular mechanisms by which miRNAs and piRNAs regulate gene expression in animal cells Showcase recent discoveries on involvement of Argonaute and Piwi proteins in different biological processes and diseases as well as their possible use in diagnosis Report breakthroughs in the use of small ncRNAs for diagnosis and personalized therapy

Download or read book Non Protein Coding RNAs written by Nils Walter and published by Springer Science & Business Media. This book was released on 2008-11-18 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers of RNA interference, Andrew Fire and Craig Mello. This prize, which follows “RNA” Nobels for splicing and RNA catalysis, highlights just one class of recently discovered non-protein coding RNAs. Remarkably, non-coding RNAs are thought to outnumber protein coding genes in mammals by perhaps as much as four-fold. In fact, it appears that the complexity of an organism correlates with the fraction of its genome devoted to non-protein coding RNAs. Essential biological processes as diverse as cell differentiation, suppression of infecting viruses and parasitic tra- posons, higher-level organization of eukaryotic chromosomes, and gene expression are found to be largely directed by non-protein coding RNAs. Currently, bioinformatic, high-throughput sequencing, and biochemical approaches are identifying an increasing number of these RNAs. Unfortunately, our ability to characterize the molecular details of these RNAs is significantly lacking. The biophysical study of these RNAs is an emergent field that is unraveling the molecular underpinnings of how RNA fulfills its multitude of roles in sustaining cellular life. The resulting understanding of the physical and chemical processes at the molecular level is critical to our ability to harness RNA for use in biotechnology and human therapy, a prospect that has recently spawned a multi-billion dollar industry.

Download or read book Computational Biology and Bioinformatics written by Ka-Chun Wong and published by CRC Press. This book was released on 2016-04-27 with total page 425 pages. Available in PDF, EPUB and Kindle. Book excerpt: The advances in biotechnology such as the next generation sequencing technologies are occurring at breathtaking speed. Advances and breakthroughs give competitive advantages to those who are prepared. However, the driving force behind the positive competition is not only limited to the technological advancement, but also to the companion data analytical skills and computational methods which are collectively called computational biology and bioinformatics. Without them, the biotechnology-output data by itself is raw and perhaps meaningless. To raise such awareness, we have collected the state-of-the-art research works in computational biology and bioinformatics with a thematic focus on gene regulation in this book. This book is designed to be self-contained and comprehensive, targeting senior undergraduates and junior graduate students in the related disciplines such as bioinformatics, computational biology, biostatistics, genome science, computer science, applied data mining, applied machine learning, life science, biomedical science, and genetics. In addition, we believe that this book will serve as a useful reference for both bioinformaticians and computational biologists in the post-genomic era.

Download or read book Long Noncoding RNAs in Plants written by Santosh Kumar Upadhyay and published by Academic Press. This book was released on 2020-11-13 with total page 390 pages. Available in PDF, EPUB and Kindle. Book excerpt: The growth of human population has increased the demand for improved yield and quality of crops and horticultural plants. However, plant productivity continues to be threatened by stresses such as heat, cold, drought, heavy metals, UV radiations, bacterial and fungal pathogens, and insect pests. Long noncoding RNAs are associated with various developmental pathways, regulatory systems, abiotic and biotic stress responses and signaling, and can provide an alternative strategy for stress management in plants. Long Noncoding RNAs in Plants: Roles in development and stress provides the most recent advances in LncRNAs, including identification, characterization, and their potential applications and uses. Introductory chapters include the basic features and brief history of development of lncRNAs studies in plants. The book then provides the knowledge about the lncRNAs in various important agricultural and horticultural crops such as cereals, legumes, fruits, vegetables, and fiber crop cotton, and their roles and applications in abiotic and biotic stress management. Includes the latest advances and research in long noncoding RNAs in plants Provides alternative strategies for abiotic and biotic stress management in horticultural plants and agricultural crops Focuses on the application and uses of long noncoding RNAs

Download or read book Cancer and Noncoding RNAs written by Jayprokas Chakrabarti and published by Academic Press. This book was released on 2017-10-13 with total page 576 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cancer and Noncoding RNAs offers an in-depth exploration of noncoding RNAs and their role in epigenetic regulation of complex human disease, most notably cancer. In addition to examining microRNAs, this volume provides a unique evaluation of more recently profiled noncoding RNAs now implicated in carcinogenesis, including lncRNAs, piRNAs, circRNAs, and tRNAs, identifying differences in function between these noncoding RNAs and how they interact with the rest of the epigenome. A broad range of chapters from experts in the field detail epigenetic regulation of various cancer types, along with recent next generation sequencing technologies, genome-wide association studies (GWAS) and bioinformatics approaches. This book will help researchers in genomic medicine and cancer biology better understand the role of noncoding RNAs in epigenetics, aiding in the development of useful biomarkers for diagnosis, prognosis and new RNA-based disease therapies. Provides a comprehensive analysis of noncoding RNAs implicated in epigenetic regulation of gene expression and chromatin dynamics Educates researchers and graduate students by highlighting, in addition to miRNAs, a range of noncoding RNAs newly associated with carcinogenesis Applies current knowledge of noncoding RNAs and epigenomics towards developing cancer and RNA-based disease therapies Features contributions by leading experts in the field

Download or read book Non coding RNAs in Complex Diseases written by Xia Li and published by . This book was released on 2018 with total page 126 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book offers an in-depth and comprehensive review on current understanding of regulatory ncRNAs in complex diseases from a view of bioinformatics. It conveys state-of-the-art bioinformatics tools and methods for ncRNAs from computational detection, functional prediction, to their roles in diseases. Computational methods used to investigate uncharacterised ncRNAs in diseases are mainly summarized in seven aspects: DNA variation of ncRNAs in diseases, prioritization of disease-related ncRNAs, dysregulation epigenetic factors that regulate ncRNA misexpression (DNA methylation and histone-modification), complex crosstalk across ncRNAs, ncRNAs acted as competing regulators to mediate the expression of protein-coding genes, non-coding RNAs mediated risk pathways,and their contributions to drug target predictions. The generally used data resources of ncRNAs are also listed in the end. This book provides important information on the current progress in the fast-moving fields of bioinformatics for regulatory ncRNAs. It provides a timely and useful reference for computational biologists, specifically with RNA interests, and other related areas.Prof. Xia Li is a Professor and the Dean of College of Bioinformatics Science and Technology, Harbin Medical University, China. Dr. Yun Xiao, Dr. Juan Xu, Dr. Shangwei Ning and Dr. Yunpeng Zhang are from College of Bioinformatics Science and Technology, Harbin Medical University, China.

Download or read book Non Coding RNAs written by Jan Barciszewski and published by Springer Science & Business Media. This book was released on 2003-08-31 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: General inspection of a role performed in the cell by RNAs allows us to distinguish three major groups of transcripts: I. protein-coding mRNAs, II. non-coding housekeeping and III. regulatory RNAs. The housekeeping RNAs include RNA classes that are generally, constitutively expressed and whose presence is required for normal function and viability of the cells. On the other hand, a group of regulatory RNAs includes RNA species that are expressed at certain stages of organism development or cell differentiation or as a response to external stimuli and can affect expression of other genes on the levels of transcription or translation. Non-coding RNA transcripts form a heterogeneous class of RNAs that can not be characterized by a single specific function. Initially, the term non-coding RNA (ncRNA) was used primarily to describe polyadenylated and a capped eukaryotic RNAs transcribed by RNA polymerase II, but lacking long open reading frames. Now, this definition can be extended to cover all RNA transcripts that do not show protein-coding capacity and is sometimes used to describe any RNA that does not encode protein, including introns. This book is an in-depth look at the function of Non-Coding RNAs and their relationship to Molecular Biology and Molecular Biology.

Download or read book Advances in Bioinformatics and Computational Biology written by Carlos E. Ferreira and published by Springer. This book was released on 2010-08-21 with total page 88 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the proceedings of the 5th Brazilian Symposium on Bioinformatics, BSB 2010, held in Rio de Janeiro, Brazil, in August/September 2010. The 5 full papers and 5 extended abstracts presented were carefully reviewed and selected for inclusion in the book. The topics of interest vary in many areas of Bioinformatics, including sequence analysis, motifs, and pattern matching; biomedical text mining; biological databases, data management, integration; biological data mining; structural, comparative, and functional genomics; protein structure, modeling and simulation; gene identification, and regulation; gene expression analysis; gene and protein interaction and networks; molecular docking; molecular evolution and phylogenetics; computational systems biology; computational proteomics; statistical analysis of molecular sequences; algorithms for problems in computational biology; as well as applications in molecular biology, biochemistry, genetics, and associated subjects.

Download or read book AGO Driven Non Coding RNAs written by Bibekanand Mallick and published by Academic Press. This book was released on 2019-01-24 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The 'RNA world' hypothesis that proposed RNA molecules as the first form of genetic material was put forwarded in the late 1980s but got impetus only recently when high-throughput sequencing technologies began unearthing new types of non-coding RNA (ncRNA) transcripts in higher eukaryotes. Till then, research on ncRNAs were primarily confined to transfer RNAs and, ribosomal RNAs, which act as the messengers of the protein synthesis and allow translation of genetic information encoded by DNA into proteins. In recent years, the integration of high-throughput genomic technologies with molecular biology and omics sciences have revolutionized the fields of ncRNA research by identifying the hidden treasures of several new types of ncRNAs encoded in the genomes of several organisms and decrypting their versatile roles in gene expression and epigenetics. Among these, two small endogenous ncRNAs, namely microRNAs (miRNAs) and piwi-interacting RNAs (piRNAs) that drive argonaute (AGO) family of proteins namely Ago and Piwi respectively and silence the expression of genes have geared up molecular and disease biology research in recent years. Both miRNAs and piRNAs are expressed in higher eukaryotes, including human and act as cellular rheostats by regulating the expression of significant fraction of genes encoded in the genomes. The aberrant expressions of these small ncRNAs within the cells cause various abnormalities and diseases including cancer. Manipulating their aberrant expression or function can serve as potential novel diagnostic/prognostic biomarkers and bring in new therapeutic strategies for multiple human diseases. This can be further translated from bench-side to clinic for improving human health. This book captures the essence of the pioneering work of some of the world's leading researchers showcasing the scientific excitements surrounding the evolving regulatory roles of miRNAs and piRNAs highlighting their potential towards the diagnosis and therapeutics of various diseases. The book is geared towards scientists, students, and will particularly appeal to active investigators in RNA biology, molecular biology, cancer research as well as clinicians and will provide them a comprehensive view of recent discoveries and research progresses to utilize miRNAs, piRNAs and their interacting proteins, Ago and Piwi for diagnosis, prognosis and therapeutics of diseases.

Download or read book RNA Bioinformatics written by Ernesto Picardi and published by Humana. This book was released on 2016-09-24 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides an overview of RNA bioinformatics methodologies, including basic strategies to predict secondary and tertiary structures, and novel algorithms based on massive RNA sequencing. Interest in RNA bioinformatics has rapidly increased thanks to the recent high-throughput sequencing technologies allowing scientists to investigate complete transcriptomes at single nucleotide resolution. Adopting advanced computational technics, scientists are now able to conduct more in-depth studies and present them to you in this book. Written in the highly successful Methods of Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and equipment, step-by-step, readily reproducible bioinformatics protocols, and key tips to avoid known pitfalls. Authoritative and practical, RNA Bioinformatics seeks to aid scientists in the further study of bioinformatics and computational biology of RNA.

Download or read book Long Non Coding RNAs written by Yi Feng and published by Humana. This book was released on 2016-01-01 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume assembles a broad spectrum of methods used in long non-coding RNAs (lncRNA) research, ranging from computational annotation of lncRNA genes to molecular and cellular analyses of the function of individual lncRNA. Long Non-Coding RNAs: Methods and Protocols also discusses methods used to study circular RNAs and RNA splicing, as well as influential findings on lncRNA in human diseases. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Thorough and cutting-edge, Long Non-Coding RNAs: Methods and Protocols is a must-have for molecular biologists, cell and developmental biologists, specialists who conduct disease-oriented research, and bioinformatics experts who seek a better understanding on lncRNA expression and function by computational analysis of the massive sequencing data that are rapidly accumulating in recent years.

Download or read book RNA Sequence Structure and Function Computational and Bioinformatic Methods written by Jan Gorodkin and published by Humana. This book was released on 2014-03-18 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The existence of genes for RNA molecules not coding for proteins (ncRNAs) has been recognized since the 1950's, but until recently, aside from the critically important ribosomal and transfer RNA genes, most focus has been on protein coding genes. However, a long series of striking discoveries, from RNA's ability to carry out catalytic function, to discovery of riboswitches, microRNAs and other ribo-regulators performing critical tasks in essentially all living organisms, has created a burgeoning interest in this primordial component of the biosphere. However, the structural characteristics and evolutionary constraints on RNA molecules are very different from those of proteins, necessitating development of a completely new suite of informatic tools to address these challenges. In RNA Sequence, Structure, Function: Computational and Bioinformatic Methods, expert researchers in the field describe a substantial and relevant fraction of these methodologies from both practical and computational/algorithmic perspectives. Focusing on both of these directions addresses both the biologist interested in knowing more about RNA bioinformatics as well as the bioinformaticist interested in more detailed aspects of the algorithms. Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results. Thorough and intuitive, RNA Sequence, Structure, Function: Computational and Bioinformatic Methods aids scientists in continuing to study key methods and principles of RNA bioinformatics.

Download or read book The Chemical Biology of Long Noncoding RNAs written by Stefan Jurga and published by Springer Nature. This book was released on 2020-10-01 with total page 545 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book offers a comprehensive and detailed overview of various aspects of long non-coding RNAs. It discusses their emerging significance in molecular medicine, ranging from human cancers to cardiovascular and metabolic diseases. Transcriptomic studies have demonstrated that the majority of genomes found in complex organisms are expressed in highly dynamic and cell-specific patterns, producing huge numbers of intergenic, antisense and intronic long non-protein-coding RNAs (lncRNAs). Thousands of lncRNAs have been identified, and unlike mRNA, they have no protein-coding capacity. A large repertoire of ncRNAs, actively transcribed from the mammalian genome, control diverse cellular processes, both in terms of development and diseases, through a variety of gene regulatory mechanisms. IncRNAs have emerged as a new paradigm in epigenetic regulation of the genome. Given its scope, the book will be of particular interest to molecular, chemical, cell and developmental biologists, as well as specialists in translational medicine involved in disease-oriented research. It also offers a valuable resource for in silico experts seeking a deeper understanding of lncRNA expression and function through computational analysis of the NGS data.